CamEds Ontology meeting 2012-07-3

BINDING AND CATALYTIC ACTIVITY

https://sourceforge.net/tracker/?func=detail&atid=440764&aid=3538813&group_id=36855

• SF item from Dianna. There's 2 types of ubiquitin ligases:
  • Where substrate binding and ubiquitin transfer are done by the same protein.
  • Where substrate binding is done by one subunit, and ubiquitin transfer is done by the second subunit.

• Can we create terms for the individual subunit activities?
• Does 'ubiquitin ligase activity' (catalysis of ....) encompass both substrate binding and ubiquitin transfer?

SWIMMING

• Where do we stand on adding in specific types of locomotion and locomotory behavior terms? (E.g. request for 'swimming'). We have 'flight' but not walking. Chris M was keen to have 'limb development' but not 'leg development'.

https://sourceforge.net/tracker/?func=detail&aid=3538830&group_id=36855&atid=440764

LIGHT ADAPTATION

• SF item from SIB: http://sourceforge.net/tracker/?func=detail&aid=3535440&group_id=36855&atid=440764

• Background: The SIB curator is annotating a rhodopsin kinase which phosphorylates opsin in cones. Phosphorylated opsin is bound by arrestin, which PREVENTS phototransduction.

Q1: Which of their requested new terms are phenotypes and which are processes?

• light adaptation: is the ability of the eye to adjust to various levels of light. (PMID:16039565, http://jgp.rupress.org/content/116/6/791.full).

• photosensitivity: Photosensitivity is the amount to which an object reacts upon receiving photons, especially visible light. (PMID:21486791).

• cone photoresponse recovery (PMID:16039565).

• Q2: Are the following terms too specific?
  • receptor phosphorylation ; GO:NEW?
  • GPCR phosphorylation ; GO:NEW?
  • GPCR kinase activity ; GO:NEW (we have rhodopsin kinase activity, already)
  • GPCR phosphorylation involved in deactivation of rhodopsin mediated signaling ; GO:NEW

• Q3: We have this term that was obsoleted: phototransduction, visible light: light adaptation ; GO:0008085.

• Q4: I'm getting a bit confused about rhodopsin vs opsin, and cones vs rods. Do the rhodopsin signaling terms just refer to rod photoreceptors (and not cone opsins)?

Suggested plan of action:

• 1. Merge:
  • rhodopsin mediated phototransduction ; GO:0009586
  • rhodopsin mediated signaling pathway ; GO:0016056

• 2. New terms:

response to light stimulus ; GO:0009416 
--[isa]response to light intensity ; GO:0009642
----[isa]light adaptation ; GO:NEW

light adaptation ; GO:NEW
Def: The process by which the eye adapts to a change/increase in illumination.

--%adaptation of rhodopsin mediated signaling ; GO:0016062
----[partof]deactivation of rhodopsin mediated signaling involved in light adaptation ; GO:NEW

deactivation of rhodopsin mediated signaling involved in light adaptation ; GO:NEW
Def: Restoring the photoreceptor cell to its unexcited state after termination of the stimulus (photon) that contributes to light adaptation at the photoreceptor level.
synonym: rhodopsin desensitization
synonym: phosphorylation-mediated desensitization [NARROW]